Why is gromacs replicating the md log files (MPI rank times)

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1

GROMACS version: 2025.2
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Hi, I am using Gromacs version 2025.2 and not sure about the error i get.

Command line:
gmx_mpi mdrun -s lignocellulose-rf.tpr -pin on -noconfout -nsteps 20000 -nstlist 200 -ntomp 1

Program: gmx mdrun, version 2025.2-EasyBuild_5.1.1
Source file: src/gromacs/utility/futil.cpp (line 357)
MPI rank: 0 (out of 72)

Fatal error:
Won’t make more than 99 backups of md.log for you.
The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.

I know it makes no sense to use more tasks for gromp but for mdrun it is starnge why i am getting this error. Currently i am using 72 tasks and 2 cpus-per-tasks.

I tried both mpirun and srun execution and get same error
mpirun gmx_mpi mdrun -s lignocellulose-rf.tpr -pin on -noconfout -nsteps 20000 -nstlist 200 -ntomp 1

Thanks in advance.

Bibek

2

GROMACS tools automatically back up output files when you try to overwrite them. This means that you ran gmx mdrun 100 times in the same directory. The simplest solution is to remove all backup files. They start with #

3

Thanks for your help, that was the problem. Sorry for that silly question, but i spent a lot of time trying to solve it. Thanks again

4

Like here you said that the gmx md production steps is running many times. then how we will run the gmx production step by distributing single job in mutiple nodes. like parallel processing of the single job.

5

I don’t understand your question. Is this is reply to the same issue that is brought up above?

6

yes similar kind of issue. i using HPC to do simulation and wants to use the multiple node for the simulation. but when i run the simulation production step, then the independent job is running on each node. so how i will resolve this issue so that i can run the single simulation by using multiple node so that the job could complete in 1 day. i am using Slurm as job scheduler for simulation production step in the HPC

7

I think you replied to the wrong thread. A likely cause is that you have configured GROMACS without an MPI library.

8

okkay , i will look for it.